I am attempting to turn off the automatic 
inclusion of the NetBeans module jars in my 
classpath for debugging and execution of a 
particular project.

For example, I choose Tools|Options and go to 
IDE Configuration|System|Filesystems 
Settings|Java Libraries|java-api.jar. I 
configure this setting to be project specific by 
picking the "define here" item on the project 
level. Then I set "Use for Execution" and "Use 
for Debugger" to false (on the capabilities 
property sheet in 3.5.1). I run the debugger and 
everything works as expected, java-api.jar is 
not in the classpath.

However, the next time I start NetBeans 
everything is back to the defaults, java-api.jar 
is used for execution and debugger again, even 
though the setting still shows up as project-
level customized (except that the customization 
seems to be "no customization").

It's as if my project-level customization never 
got saved or loaded.

This problem occurs in both 3.5.1 and the latest 
3.6 QA build.